On 15/10/16 10:02, Thejus Kartha wrote:
I was trying to calculate the dielectric constant of my system (1,4-dioxane and 
water), and I have encountered some problems. I gave the command to calculate 
dipole moment and related data, since it is a prerequisite for the dielectric 

gmx dipoles -f sol1ns2.trr -s sol1ns2.tpr -o dipac.xvg -eps diel_1.xvg -a 
muavers.xvg -d dipdist.xvg -P 1 -corr total -c dipcorr.xvg
which ran perfectly, providing me with 5 .xvg files, as it should. Now, 
following this, I typed in:
gmx dielectric -f dipcorr.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg
which gave me the error and the 
WARNING: non-polarizable models can never yield an infinite
dielectric constant that is different from 1. This is incorrect
in the reference given above 
*** Error in `gmx': malloc(): smallbin double linked list corrupted: 
0x00000000011191f0 ***
Aborted (core dumped)
 you please let me know where I am going wrong? I understand that there's 
something called the reaction field epsilon value, which is where I could have 
gone wrong, as I did not specify it in the first command.

Thanks in advance,Thejus Kartha.

This has been fixed in the latest gromacs 5.1.4 and 2016. If you just want the dielectric constant at zero frequency you don't need to run gmx dielectric at all however.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
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